Robert J. Robbins is a biologist, an educator, a science administrator, a
publisher, an information technologist, and an IT leader and manager who
specializes in advancing biomedical knowledge and supporting education
through the application of information technology.
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Bibliographies

(with links to sources)

Keeping up with the literature can be challenging. Here we offer
several automatically-created bibliographies on selected topics, with
links out to the original document (via the publisher's DOI), to
PubMed, to Google Scholar, etc.

The bibliographies are updated regularly and are sorted to show the
most recent at the top. For long bibliographies the link is to a page
containing only the most recent 100 entries, with a Bibliography
Options menu allowing access to a page with the remaining
entries. These additional pages can be very large and slow to load,
but they can be valuable if you are interested in a comprehensive
listing.
The options menu also allows you to download the entire bibliography
in bibtex format, for easy loading into reference-management software.
The topics are chosen because they interest me, but I would be
happy to consider adding additional topics.
Contact me
with any suggestions.

Wikipedia:
The species problem is the set of questions that arises when biologists
attempt to define what a species is. Such a definition is called a species
concept; there are at least 26 recognized species concepts. A species
concept that works well for sexually reproducing organisms such as birds is
useless for species that reproduce asexually, such as bacteria. The scientific
study of the species problem has been called microtaxonomy.
One common, but sometimes difficult, question is how best to decide which
species an organism belongs to, because reproductively isolated groups may
not be readily recognizable, and cryptic species may be present. There is a
continuum from reproductive isolation with no interbreeding, to panmixis,
unlimited interbreeding. Populations can move forward or backwards along this
continuum, at any point meeting the criteria for one or another species
concept, and failing others.
Many of the debates on species touch on philosophical issues, such as
nominalism and realism, and on issues of language and cognition.
The current meaning of the phrase "species problem" is quite different
from what Charles Darwin and others meant by it during the 19th and early
20th centuries. For Darwin, the species problem was the question of how
new species arose. Darwin was however one of the first people to question
how well-defined species are, given that they constantly change.

In 1977,
Carl Woese and George Fox
applied molecular techniques to biodiversity
and discovered that life on Earth consisted of three, not two (prokaryotes and
eukaryotes), major lineages,
tracing back nearly to the very origin of life on Earth. The third lineage
has come to be known as the Archaea. Organisms now considered Archaea were
originally thought to be a kind of prokaryote, but Woese and Fox showed that they
were as different from prokaryotes as they were from eukaryotes. To understand life on Earth
one must also understand the
Archaea
.

PUBMED QUERY: archaea[TITLE] OR archaebacteria[TITLE] NOT pmcbook NOT ispreviousversion

If evolution is the only light in which biology makes sense, and if variation is
the raw material upon which selection works, then variety is not merely the
spice of life, it is the essence of life — the sine qua non without which
life could not exist. To understand biology, one must understand its diversity.
Historically, studies of biodiversity were directed primarily at the realm
of multicellular eukaryotes, since few tools existed to allow the study of
non-eukaryotes. Because metagenomics allows the study of intact microbial
communities, without requiring individual cultures, it provides a tool for
understanding this huge, hitherto invisible pool of biodiversity, whether it
occurs in free-living communities or in commensal microbiomes associated with
larger organisms.

The pathology-inducing genes of O157:H7 appear to have been acquired,
likely via prophage, by a nonpathogenic E. coli ancestor,
perhaps 20,000 years ago. That is, horizontal gene transfer (HGT) can
lead to the profound phenotypic change from benign commensal to lethal
pathogen. "Horizontal" in this context refers to the lateral or
"sideways" movement of genes between microbes via mechanisms not
directly associated with reproduction. HGT among prokaryotes can occur
between members of the same "species" as well as between microbes
separated by vast taxonomic distances. As such, much prokaryotic
genetic diversity is both created and sustained by high levels of HGT.
Although HGT can occur for genes in the core-genome component of a
pan-genome, it occurs much more frequently among genes in the
optional, flex-genome component. In some cases, HGT has become so
common that it is possible to think of some "floating" genes more as
attributes of the environment in which they are useful rather than as
attributes of any individual bacterium or strain or "species" that
happens to carry them. For example, bacterial plasmids that occur in
hospitals are capable of conferring pathogenicity on any bacterium
that successfully takes them up. This kind of genetic exchange can
occur between widely unrelated taxa.

PUBMED QUERY: "(horizontal or lateral) "gene transfer"" NOT pmcbook NOT ispreviousversion NOT pmcbook NOT ispreviousversion

﻿Holobionts are assemblages of different species that form ecological units.
Lynn Margulis proposed that any physical association between individuals of
different species for significant portions of their life history is a symbiosis.
All participants in the symbiosis are bionts, and therefore the resulting
assemblage was first coined a holobiont by Lynn Margulis in 1991 in the book
Symbiosis as a Source of Evolutionary Innovation.
Holo is derived from the Ancient Greek word ὅλος (hólos) for “whole”. The entire
assemblage of genomes in the holobiont is termed a hologenome.

PUBMED QUERY: holobiont OR hologenome NOT pmcbook NOT ispreviousversion

While genomics is the study of DNA extracted from individuals — individual
cells, tissues, or organisms — metagenomics is a more recent refinement that
analyzes samples of pooled DNA taken from the environment, not from an individual.
Like genomics, metagenomic methods have great potential in many areas of biology,
but none so much as in providing access to the hitherto invisible world of
unculturable microbes, often estimated to comprise 90% or more of bacterial species
and, in some ecosystems, the bulk of the biomass. A recent
describes how this new science of metagenomics is beginning to reveal the secrets
of our microbial world: The opportunity that stands before microbiologists
today is akin to a reinvention of the microscope in the expanse of research
questions it opens to investigation. Metagenomics provides a new way of examining
the microbial world that not only will transform modern microbiology but has the
potential to revolutionize understanding of the entire living world. In metagenomics,
the power of genomic analysis is applied to entire communities of microbes,
bypassing the need to isolate and culture individual bacterial community members.

PUBMED QUERY: metagenomic OR metagenomics OR metagenome NOT pmcbook NOT ispreviousversion

Although the enforced stability of genomic content is ubiquitous among
MCEs, the opposite is proving to be the case among prokaryotes, which
exhibit remarkable and adaptive plasticity of genomic content. Early
bacterial whole-genome sequencing efforts discovered that whenever a
particular "species" was re-sequenced, new genes were found that had
not been detected earlier — entirely new genes, not merely new alleles.
This led to the concepts of the bacterial core-genome, the set of
genes found in all members of a particular "species", and the
flex-genome, the set of genes found in some, but not all members of
the "species". Together these make up the species' pan-genome.

PUBMED QUERY: pangenome or "pan-genome" or "pan genome" NOT pmcbook NOT ispreviousversion

Wikipedia: Microbial Ecology
(or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses.
Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

Wikipedia: Biofilm
A biofilm is any group of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPS). The EPS components are produced by the cells within the biofilm and are typically a polymeric conglomeration of extracellular DNA, proteins, and polysaccharides. Because they have three-dimensional structure and represent a community lifestyle for microorganisms, biofilms are frequently described metaphorically as cities for microbes.
Biofilms may form on living or non-living surfaces and can be prevalent in natural, industrial and hospital settings. The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of the same organism, which, by contrast, are single-cells that may float or swim in a liquid medium. Biofilms can be present on the teeth of most animals as dental plaque, where they may cause tooth decay and gum disease.
Microbes form a biofilm in response to many factors, which may include cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, or in some cases, by exposure of planktonic cells to sub-inhibitory concentrations of antibiotics. When a cell switches to the biofilm mode of growth, it undergoes a phenotypic shift in behavior in which large suites of genes are differentially regulated.

It is well known that relative size greatly affects how
organisms interact with the world. Less well known, at least among
biologists, is that at sufficiently small sizes, mechanical
interaction with the environment becomes difficult and then virtually
impossible. In fluid dynamics, an important dimensionless parameter is
the Reynolds Number (abbreviated Re), which is the ratio of
inertial to viscous forces affecting the movement of objects in a
fluid medium (or the movement of a fluid in a pipe). Since Re is
determined mainly by the size of the object (pipe) and the properties
(density and viscosity) of the fluid, organisms of different sizes
exhibit significantly different Re values when moving through air or
water. A fish, swimming at a high ratio of inertial to viscous forces,
gives a flick of its tail and then glides for several body lengths. A
bacterium, "swimming" in an environment dominated by viscosity,
possesses virtually no inertia. When the bacterium stops moving its
flagellum, the bacterium "coasts" for about a half of a microsecond,
coming to a stop in a distance less than a tenth the diameter of a
hydrogen atom. Similarly, the movement of molecules (nutrients toward,
wastes away) in the vicinity of a bacterium is dominated by diffusion.
Effective stirring — the generation of bulk flow through
mechanical means — is impossible at very low Re. An
understanding of the constraints imposed by life at low Reynolds
numbers is essentially for understanding the prokaryotic biosphere.

Symbiosis refers to an interaction between two or more
different organisms living in close physical association, typically to
the advantage of both. Symbiotic relationships were once thought to be
exceptional situations. Recent studies, however, have shown that
every multicellular eukaryote exists in a tight symbiotic
relationship with billions of microbes. The associated microbial ecosystems
are referred to as microbiome
and the combination of a multicellular organism and its microbiota has been
described as a
holobiont.
It seems "we are all lichens now."

A symbiotic relationship in which one of the partners lives within the other,
especially if it lives within the cells of the other, is known as endosymbiosis.
Mitochondria, chloroplasts, and perhaps other cellular organelles
are believed to have originated from a form of endosymbiosis. The endosymbiotic
origin of eukaryotes seems to have been a biological singularity — that is,
it happened once, and only once, in the history of life on Earth.

WIKIPEDIA: Wolbachia is a genus of bacteria which "infects" (usually as
intracellular symbionts) arthropod species,
including a high proportion of insects, as well as some nematodes. It is one of
the world's most common parasitic microbes and is possibly the most common
reproductive parasite in the biosphere. Its interactions with its hosts are
often complex, and in some cases have evolved to be mutualistic rather than
parasitic. Some host species cannot reproduce, or even survive, without Wolbachia
infection. One study concluded that more than 16% of neotropical insect species
carry bacteria of this genus, and as many as 25 to 70 percent of all insect
species are estimated to be potential hosts. Wolbachia also harbor a temperate
bacteriophage called WO. Comparative sequence analyses of bacteriophage WO
offer some of the most compelling examples of large-scale horizontal gene
transfer between Wolbachia coinfections in the same host. It is the first
bacteriophage implicated in frequent lateral transfer between the genomes of
bacterial endosymbionts. Gene transfer by bacteriophages could drive significant
evolutionary change in the genomes of intracellular bacteria that were previously
considered highly stable or prone to loss of genes overtime. Outside of insects,
Wolbachia infects a variety of isopod species, spiders, mites, and many species
of filarial nematodes (a type of parasitic worm), including those causing
onchocerciasis ("River Blindness") and elephantiasis in humans as well as
heartworms in dogs. Not only are these disease-causing filarial worms
infected with Wolbachia, but Wolbachia seem to play an inordinate role in these
diseases. A large part of the pathogenicity of filarial nematodes is due to
host immune response toward their Wolbachia. Elimination of Wolbachia from
filarial nematodes generally results in either death or sterility of the nematode.

For many multicellular organisms, a microscopic study shows that microbial cells
outnumber host cells by perhaps ten to one. Until recently, these abundant
communities of host-associated microbes were largely unstudied, often for lack
of analytical tools or conceptual frameworks. The advent of new tools is rendering
visible this previously ignored biosphere and the results have been startling.
Many facets of host biology have proven to be profoundly affected by the
associated microbiomes. As a result, several large-scale projects — such as
the
Human Microbiome Project
— have been undertaken to jump start an understanding
of this critical component of the biosphere.

It has long been known that every multicellular organism
coexists with large prokaryotic ecosystems — microbiomes —
that completely cover its surfaces, external and internal. Recent
studies have shown that these associated microbiomes are not mere
contamination, but instead have profound effects upon the function and
fitness of the multicellular organism. We now know that all MCEs are
actually functional composites, holobionts, composed of more
prokaryotic cells than eukaryotic cells and expressing more
prokaryotic genes than eukaryotic genes. A full understanding of the
biology of "individual" eukaryotes will now depend on an understanding
of their associated microbiomes.

The human microbiome is the set of all microbes that live on or in humans.
Together, a human body and its associated microbiomes constitute a human
holobiont.
Although a human holobiont is mostly mammal by weight, by cell count it is
mostly microbial. The number of microbial genes in the associated microbiomes far
outnumber the number of human genes in the human genome. Just as humans (and
other multicellular eukaryotes) evolved in the constant presence of gravity,
so they also evolved in the constant presence of microbes. Consequently,
nearly every aspect of human biology has evolved to deal with, and to take
advantage of, the existence of associated microbiota. In some cases, the
absence of a "normal microbiome" can cause disease, which can be treated
by the transplant of a correct microbiome from a healthy donor. For example,
fecal transplants are an effective treatment for chronic diarrhea from
over abundant Clostridium difficile bacteria in the gut.

The small bobtail squid (Euprymna scolopes) has a mutually beneficial
relationship with bacteria
called Vibrio fischeri that live on the squid's underside. The bacteria
allow the squid to produce light, which then allows the squid to escape from
things that might want to eat it. "The squid emit ventral luminescence that is
often very, very close to the quality of light coming from the moon and stars
at night," explains Margaret McFall-Ngai, Margaret McFall-Ngai, professor of medical
microbiology and immunology at the University of Wisconsin-Madison.
For fish looking up from below for something to eat, the squid are camouflaged
against the moon or the starlight because they don't cast a shadow. "It's like a
'Klingon' cloaking device," she notes. But the Vibrio fischeri don't stay
in the squid continuously. Every day, in response to the light cue of dawn, the
squid vents 90 percent of the bacteria back into the seawater. "And then, while
it's sitting quiescent in the sand, the bacteria grow up in the crypt so that
when [the squid] comes out in the evening, it will have a full complement of
luminous Vibrio fischeri," says McFall-Ngai.

PUBMED QUERY: (squid OR euprymna) AND (vibrio OR symbiosis OR symbiotic OR endosymbiont) NOT pmcbook NOT ispreviousversion

The evolutionary origin of eukaryotes is a critically important, yet
poorly understood event in the history of life on earth. The
endosymbiotic origin of mitochondria allowed cells to become
sufficiently large that they could begin to interact mechanically with
their surrounding environment, thereby allowing evolution to create
the visible biosphere of multicellular eukaryotes.

PUBMED QUERY: ("origin of eukaryotes"[TIAB] OR "appearance of eukaryotes"[TIAB] OR "evolution of eukaryotes[TIAB]") NOT pmcbook NOT ispreviousversion

The endosymbiotic hypothesis for the origin of mitochondria (and
chloroplasts) suggests that mitochondria are descended from
specialized bacteria (probably purple nonsulfur bacteria) that somehow
survived endocytosis by another species of prokaryote or some other
cell type, and became incorporated into the cytoplasm.

PUBMED QUERY: mitochondria AND evolution NOT pmcbook NOT ispreviousversion

Mitochondria are the energy-producing "engines" that provide the power
to drive eukaryotic cells. The energy output of hundreds, or
thousands, of mitochondria allowed eukaryotic cells to increase in
size 1000-fold, or more, over the size of prokaryotics cells. This
increase in size allowed an escape from the constraints of low
Reynolds numbers and, for the first time, life could function in a way
where mechanism, and thus morphology, mattered. Evolution began to
shape morphology, allowing the emergence of the multicellular
eukaryotic biosphere — the visible living world.

PUBMED QUERY: mitochondria AND evolution AND (energetics OR "energy metabolism") NOT pmcbook NOT ispreviousversion

﻿Wikipedia:
A telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos (τέλος) "end" and merοs (μέρος, root: μερ-) "part". For vertebrates, the sequence of nucleotides in telomeres is TTAGGG, with the complementary DNA strand being AATCCC, with a single-stranded TTAGGG overhang. This sequence of TTAGGG is repeated approximately 2,500 times in humans. In humans, average telomere length declines from about 11 kilobases at birth to less than 4 kilobases in old age,[3] with average rate of decline being greater in men than in women.
During chromosome replication, the enzymes that duplicate DNA cannot continue their duplication all the way to the end of a chromosome, so in each duplication the end of the chromosome is shortened (this is because the synthesis of Okazaki fragments requires RNA primers attaching ahead on the lagging strand). The telomeres are disposable buffers at the ends of chromosomes which are truncated during cell division; their presence protects the genes before them on the chromosome from being truncated instead. The telomeres themselves are protected by a complex of shelterin proteins, as well as by the RNA that telomeric DNA encodes.

PUBMED QUERY: telomere[title] OR telomeres[title] NOT pmcbook NOT ispreviousversion

In the small "Fly Room" at Columbia University, T. H. Morgan and his
students, A. H. Sturtevant, C. B. Bridges, H. J. Muller, carried out
the work that laid the foundations of modern, chromosomal genetics.
The excitement of those times, when the whole field of genetics was
being created, is captured in this book, written by one of those
present at the beginning. In a time when genomics and genetics maps
are discussed almost daily in the popular press, it is worth
remembering that the world's first genetic map was created in 1913 by
A. H. Sturtevant, then a sophomore in college. In 1933, Morgan
received the Nobel Prize in medicine, for his "discoveries concerning
the role played by the chro- mosome in heredity." In the 67 years
since, genetics has continued to advance, leaving behind a fascinating
history. The year 2000 was the 100th anniversary of the founding of
modern genetics with the rediscovery of Mendel' work and it is the
year in which the full DNA sequence of the Drosophila genome was
obtained. The fruit fly is still at the center of genetic research,
just as it was in 1910 when work first began in Morgan's fly room.

PUBMED QUERY: 1890:1932[PDAT] AND (drosophila OR gene OR genetic OR map OR chromosome OR mutamnt OR mutation) AND ( "morgan th"[author] OR "morgan lv"[author] OR "sturtevant AH"[author] OR "bridges CB"[author] OR "muller HJ"[author] ) NOT pmcbook NOT ispreviousversion

In 1865, Gregor Mendel reported the results of his experiments with
peas and in so doing laid the foundations of what has become the
modern science of genetics. There are few examples of entire fields
having been so clearly founded upon the works of one man.

PUBMED QUERY: mendel[title] AND (gregor OR brno OR versuche OR darwin OR "father of genetics") NOT "James Ross" NOT Antarctic NOT pmcbook NOT ispreviousversion

In 1936, R. A. Fisher noted that Mendel's results seem to come too
close to the expected value too often, leading him to conclude "the
general level of agreement between Mendel's expectations and his
reported results shows that it is closer than would be expected in the
best of several thousand repetitions. The data have evidently been
sophisticated systematically..." That is, Mendel's data had been
fiddled with. A small industry has grown up, with various authors
taking sides on the controversy.

PUBMED QUERY: (mendel[TITLE] OR mendelian[TITLE]) AND (cheat OR "too good"[TITLE] OR fisher OR controversy OR controversies) NOT (Humans[MESH] OR rats[MESH] OR Software[MESH] OR "Mendelian randomization") NOT pmcbook NOT ispreviousversion

Wikipedia:
Classical genetics is often referred to as the oldest form of genetics, and
began with Gregor Mendel's experiments that formulated and defined a
fundamental biological concept known as Mendelian Inheritance. Mendelian
Inheritance is the process in which genes and traits are passed from a set
of parents to their offspring. These inherited traits are passed down
mechanistically with one gene from one parent and the second gene from another
parent in sexually reproducing organisms. This creates the pair of genes in
diploid organisms. Gregor Mendel started his experimentation and study of
inheritance with phenotypes of garden peas and continued the experiments with
plants. He focused on the patterns of the traits that were being passed down
from one generation to the next generation. This was assessed by test-crossing
two peas of different colors and observing the resulting phenotypes. After
determining how the traits were likely inherited, he began to expand the amount
of traits observed and tested and eventually expanded his experimentation by
increasing the number of different organisms he tested.

PUBMED QUERY: 1890:1938[PDAT] AND (genetic OR gene OR genes OR genetics OR heredity OR inheritance OR mutation OR chromosome OR mendel) NOT pmcbook NOT ispreviousversion

Wikipedia:
Drosophila is a genus of flies, belonging to the family Drosophilidae, whose
members are often called "small fruit flies" or (less frequently) pomace flies,
vinegar flies, or wine flies, a reference to the characteristic of many species
to linger around overripe or rotting fruit.
One species of Drosophila in particular, D. melanogaster, has been
heavily used in research in genetics and is a common model organism in
developmental biology. The terms "fruit fly" and "Drosophila" are often used
synonymously with D. melanogaster in modern biological literature.
The entire genus, however, contains more than 1,500 species and is very diverse
in appearance, behavior, and breeding habitat.
D. melanogaster is a popular experimental animal because it is easily
cultured en masse out of the wild, has a short generation time, and mutant
animals are readily obtainable. In 1906, Thomas Hunt Morgan began his work on
D. melanogaster and reported his first finding of a 'white' (eyed)
mutant in 1910 to the academic community. He was in search of a model organism
to study genetic heredity and required a species that could randomly acquire
genetic mutation that would visibly manifest as morphological changes in the
adult animal. His work on Drosophila earned him the 1933 Nobel Prize in Medicine
for identifying chromosomes as the vector of inheritance for genes.

PUBMED QUERY: 1890:1953[PDAT] AND drosophila NOT pmcbook NOT ispreviousversion

Wikipedia:
We now know that, in biology, a mutation is the process that produces heritable
change via the permanent alteration of the nucleotide sequence of the genome of
an organism, virus, or extrachromosomal DNA or other genetic elements.
Mutations result from errors during DNA replication
or other types of damage to DNA (such as may be caused by exposure to radiation
or carcinogens), which then may undergo error-prone repair, or cause an error
during other forms of repair, or else may cause an error during replication.
Mutations may also result from insertion or deletion of segments of DNA due to
mobile genetic elements. Mutations may or may not produce discernible changes
in the observable characteristics (phenotype) of an organism. Mutations play a
part in both normal and abnormal biological processes including: evolution,
cancer, and the development of the immune system, including junctional diversity.
In the early days of classical genetics, work to characterize, model, and
understand the phenomenology of mutation were critically important for
developing the foundations of modern molecular genetics.

PUBMED QUERY: 1859:1953[PDAT] AND (mutation OR mutant OR mutagen) NOT pmcbook NOT ispreviousversion

The LTER Network:
The US. long-term ecological research network consists of 28 sites with a rich history of ecological inquiry, collaboration across a wide range of research topics, and engagement with students, educators, and community members.
Bringing together diverse groups of researchers with sustained data collection, ecosystem manipulation experiments, and modeling, these sites allow scientists to apply new tools and explore new questions in systems where the context is well understood, shared, and thoroughly documented.

PUBMED QUERY: "Long Term Ecological Research" OR LTER NOT pmcbook NOT ispreviousversion

Wikipedia: Ecological Informatics
Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics.
A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses.
Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web.
Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are the National Science Foundation's
Datanet
,
DataONE
and Data Conservancy projects.

PUBMED QUERY: "ecology OR ecological" and ("data management" or informatics) NOT pmcbook NOT ispreviousversion

Standard Definition:Invasive species are plants, animals, or pathogens that are non-native (or alien)
to the ecosystem under consideration and whose introduction causes or is likely
to cause harm. Although that definition allows a logical possibility that some species
might be non-native and harmless, most of time it seems that
invasive species
and
really bad critter (or weed) that should be eradicated
are seen as equivalent phrases.
But, there is a big conceptual problem with that notion: every species in every ecosystem
started out in that ecosystem as an invader. If there were no invasive species,
all of Hawaii would be nothing but bare volcanic rock. Without an invasion
of species onto land, there would be no terrestrial ecosystems at all. For the
entire history of life on Earth, the biosphere has responded to perturbation and to
opportunity with evolutionary innovation and with physical movement.
While one may raise economic or aesthetic arguments against invasive species, it is
impossible to make such an argument on scientific grounds. Species movement —
the occurrence of invasive species — is the way the biosphere responds to
perturbation. One might even argue that species movement is the primary,
short-term "healing" mechanism employed by the biosphere to respond to perturbation —
to "damage."
As with any healing process, the short-term effect may be aesthetically
unappealing (who thinks scabs are appealing?), but the long-term effects can be glorious.

Sociobiology
is a field of scientific study that is based on the hypothesis that social behavior has resulted from evolution and attempts to examine and explain social behavior within that context.
Sociobiology investigates social behaviors, such as mating patterns, territorial fights, pack hunting, and the hive society of social insects. It argues that just as selection pressure led to animals evolving useful ways of interacting with the natural environment, it led to the genetic evolution of advantageous social behavior.
While the term "sociobiology" can be traced to the 1940s, the concept did not gain major recognition until the publication of Edward O. Wilson's book Sociobiology: The New Synthesis in 1975.

Wikipedia: Kin selection is the evolutionary strategy that favours the reproductive success of an organism's relatives, even at a cost to the organism's own survival and reproduction. Kin altruism is altruistic behaviour whose evolution is driven by kin selection. Kin selection is an instance of inclusive fitness, which combines the number of offspring produced with the number an individual can produce by supporting others, such as siblings. Charles Darwin discussed the concept of kin selection in his 1859 book, The Origin of Species, where he reflected on the puzzle of sterile social insects, such as honey bees, which leave reproduction to their mothers, arguing that a selection benefit to related organisms (the same "stock") would allow the evolution of a trait that confers the benefit but destroys an individual at the same time. R.A. Fisher in 1930 and J.B.S. Haldane in 1932 set out the mathematics of kin selection, with Haldane famously joking that he would willingly die for two brothers or eight cousins. In 1964, W.D. Hamilton popularised the concept and the major advance in the mathematical treatment of the phenomenon by George R. Price which has become known as "Hamilton's rule". In the same year John Maynard Smith used the actual term kin selection for the first time. According to Hamilton's rule, kin selection causes genes to increase in frequency when the genetic relatedness of a recipient to an actor multiplied by the benefit to the recipient is greater than the reproductive cost to the actor.

The
Genomic Standards Consortium (GSC)
is an open-membership working body formed
in September 2005. The aim of the GSC is making genomic data discoverable. The
GSC enables genomic data integration, discovery and comparison through international
community-driven standards.

PUBMED QUERY: ("genomic standards consortium" AND GSC OR RCN4GSC) NOT pmcbook NOT ispreviousversion

The Fred Hutchinson Cancer Research Center began in 1975, with critical help from Washington State's U.S. Senator Warren Magnuson.
Fred Hutch quickly became the permanent home to Dr. E. Donnall Thomas, who had spent decades developing an innovative treatment for leukemia and other blood cancers. Thomas and his colleagues were working to cure cancer by transplanting human bone marrow after otherwise lethal doses of chemotherapy and radiation. At the Hutch, Thomas improved this treatment and readied it for widespread use. Since then, the pioneering procedure has saved hundreds of thousands of lives worldwide.
While improving bone marrow transplantation remains central to Fred Hutch's research, it is now only part of its efforts. The Hutch is home to five scientific divisions, three Nobel laureates and more than 2,700 faculty, who collectively have published more than 10,000 scientific papers, presented here as a full bibliography.

NOTE: From 1995 to 2009 I served as the Hutch's vice president for information technology — hence my interest in the organization. Although my role was in the admin division, if you dig through this bibliography, you will find a couple of papers with me as an author.

Wikipedia:
Misophonia, literally "hatred of sound," was proposed in 2000 as a condition in which negative emotions, thoughts, and physical reactions are triggered by specific sounds. It is also called "select sound sensitivity syndrome" and "sound-rage." Misophonia has no classification as an auditory, neurological, or psychiatric condition, there are no standard diagnostic criteria, it is not recognized in the DSM-IV or the ICD-10, and there is little research on its prevalence or treatment. Proponents suggest misophonia can adversely affect ability to achieve life goals and to enjoy social situations. Treatment consists of developing coping strategies such as cognitive behavioral therapy and exposure therapy. As of 2016 the literature on misophonia was very limited (see below). Some small studies show that people with misophonia generally have strong negative feelings, thoughts, and physical reactions to specific sounds, which the literature calls "trigger sounds." One study found that around 80% of the sounds were related to the mouth (eating, yawning, etc.), and around 60% were repetitive.

Wikipedia: Hoopoes
are colourful birds found across Afro-Eurasia, notable for their
distinctive "crown" of feathers. Three living and one extinct species are
recognized, though for many years all were lumped as a single species —
Upupa epops. Formerly considered a single species, the hoopoe has
been split into three separate species: the Eurasian hoopoe, Madagascan
hoopoe and the resident African hoopoe. One accepted separate species,
the Saint Helena hoopoe, lived on the island of St Helena but became
extinct in the 16th century. Hoopoes are distinctive birds and have made
a cultural impact over much of their range. They were considered sacred
in Ancient Egypt, and were "depicted on the walls of tombs and temples".
At the Old Kingdom, the hoopoe was used in the iconography as a symbolic
code to indicate the child was the heir and successor of his father. They
achieved a similar standing in Minoan Crete. In the Torah, Leviticus 11:13-19,
hoopoes were listed among the animals that are detestable and should not
be eaten. They are also listed in Deuteronomy as not kosher. Hoopoes also
appear in the Quran and is known as the "hudhud", in Surah Al-Naml 27:20-22:
"And he Solomon sought among the birds and said: How is it that I see not
the hoopoe, or is he among the absent? I verily will punish him with hard
punishment or I verily will slay him, or he verily shall bring me a plain
excuse. But he [the hoopoe] was not long in coming, and he said: I have
found out (a thing) that thou apprehendest not, and I come unto thee from
Sheba with sure tidings." The sacredness of the Hoopoe and connection with
Solomon and the Queen of Sheba is mentioned in passing in Rudyard Kipling's
"The Butterfly that Stamped." Islamic literature also states that a hoopoe
saved Moses and the children of Israel from being crushed by the giant Og
after crossing the Red Sea. The hoopoe is the king of the birds in the
Ancient Greek comedy The Birds by Aristophanes.
Hoopoes have well-developed anti-predator defences in the nest. The
uropygial gland of the incubating and brooding female is quickly modified
to produce a foul-smelling liquid, and the glands of nestlings do so as
well. These secretions are rubbed into the plumage. The secretion, which
smells like rotting meat, is thought to help deter predators, as well as
deter parasites and possibly act as an antibacterial agent. The secretions
stop soon before the young leave the nest. From the age of six days,
nestlings can also direct streams of faeces at intruders, and will hiss
at them in a snake-like fashion.

Some mineral solutes precipitate to form crystals
in urine; these crystals may aggregate and grow to macroscopic
size, at which time they are known as uroliths (calculi or
stones). Mechanisms involved in stone formation are
incompletely understood in dogs and cats. Regardless of the
underlying mechanism(s), uroliths are not produced unless
sufficiently high urine concentrations of urolith-forming
constituents exist and transit time of crystals within the
urinary tract is prolonged. Clinical signs associated with
urolithiasis are seldom caused by microscopic crystals. However,
formation of macroscopic uroliths in the lower urinary tract
that interfere with the flow of urine and/or irritate the
mucosal surface often results in dysuria, hematuria, and
stranguria. Urethral obstruction is common in male dogs and
cats. It may occur suddenly or may develop throughout days or
weeks. Initially, the animal may frequently attempt to urinate
and produce only a fine stream, a few drops, or nothing. Animals
may also exhibit extreme pain manifested by crying out when
attempting to urinate. Complete obstruction causes uremia within
36–48 hr, which leads to depression, anorexia, vomiting, diarrhea,
dehydration, coma, and death within ~72 hr.

NOTE:
Urethral obstruction is an emergency condition, and treatment
should begin immediately.

PUBMED QUERY: (canine OR feline) and (urolithiasis) NOT pmcbook NOT ispreviousversion

Wikipedia: Calcium Metabolism
— everybody knows that osteoporosis is a huge threat and that the best way
to reduce the risk of osteoporosis is to take lots of dietary calcium supplements
and vitamin D pills.

OK, exercise is good, too, but that can involve actually
breaking a sweat — something that not everyone wants to do.

But, did you also know that hypercalciuria (too much secreted calcium in the urine) is
associated with a significant increase in the risk for kidney stones? And, you can
easily get hypercalciuria if you pop too many calcium-supplement pills.
Hmmmm.
Nice choice, break a hip or pass kidney stones... What to do? As with most things
biological, reality lies somewhere in the trade-off zone. A quick look at the
literature dealing with calciuria and kidney stones is one way to start.

PUBMED QUERY: (calciuria OR "calcium metabolism") AND (urolith or "kidney stone" or "kidney stones" or "bladder stones" or stones) NOT pmcbook NOT ispreviousversion

Wikipedia:
Neanderthals or Neandertals — named for the Neandertal region in Germany — were a species or subspecies of archaic human, in the genus Homo. Neanderthals became extinct around 40,000 years ago. They were closely related to modern humans, sharing 99.7% of DNA. Remains left by Neanderthals include bone and stone tools, which are found in Eurasia, from Western Europe to Central and Northern Asia. Neanderthals are generally classified by paleontologists as the species Homo neanderthalensis, having separated from the Homo sapiens lineage 600,000 years ago, but a minority consider them to be a subspecies of Homo sapiens (Homo sapiens neanderthalensis). Several cultural assemblages have been linked to the Neanderthals in Europe. The earliest, the Mousterian stone tool culture, dates to about 160,000 years ago. Late Mousterian artifacts were found in Gorham's Cave on the south-facing coast of Gibraltar.
Compared to Homo sapiens, Neanderthals had a lower surface-to-volume ratio, with shorter legs and a bigger body, in conformance with Bergmann's rule, as an energy-loss reduction adaptation to life in a high-latitude (i.e. seasonally cold) climate. Their average cranial capacity was notably larger than typical for modern humans: 1600 cm3 vs. 1250-1400 cm3. The
Neanderthal genome project
published papers in 2010 and 2014 stating that Neanderthals contributed to the DNA of modern humans, including most humans outside sub-Saharan Africa, as well as a few populations in sub-Saharan Africa, through interbreeding, likely between 50,000 and 60,000 years ago.

PUBMED QUERY: Neanderthal OR Neandertal NOT pmcbook NOT ispreviousversion

Wikipedia:
The Denisovans are an extinct species or subspecies of human in the genus Homo. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans. Two teeth belonging to different members of the same population have since been reported. In November 2015, a tooth fossil containing DNA was reported to have been found and studied. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known. Analysis of the mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from the mtDNAs of Neanderthals and modern humans. Subsequent study of the nuclear genome from this specimen suggests that Denisovans shared a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some modern humans. A comparison with the genome of a Neanderthal from the same cave revealed significant local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, while evidence was also detected of interbreeding with an as yet unidentified ancient human lineage.

Wikipedia:
Homo floresiensis ("Flores Man"; nicknamed "hobbit" for its small stature) is an extinct species in the genus Homo.
The remains of an individual that would have stood about 3.5 feet (1.1 m) in height were discovered in 2003 at Liang Bua on the island of Flores in Indonesia. Partial skeletons of nine individuals have been recovered, including one complete skull, referred to as "LB1".These remains have been the subject of intense research to determine whether they represent a species distinct from modern humans. This hominin had originally been considered to be remarkable for its survival until relatively recent times, only 12,000 years ago. However, more extensive stratigraphic and chronological work has pushed the dating of the most recent evidence of their existence back to 50,000 years ago. Their skeletal material is now dated to from 100,000 to 60,000 years ago; stone tools recovered alongside the skeletal remains were from archaeological horizons ranging from 190,000 to 50,000 years ago.
Fossil teeth and a partial jaw from hominins believed ancestral to H. floresiensis were discovered in 2014 and described in 2016. These remains are from a site on Flores called Mata Menge, about 74 km from Liang Bua. They date to about 700,000 years ago and are even smaller than the later fossils. The form of the fossils has been interpreted as suggesting that they are derived from a population of H. erectus that arrived on Flores about a million years ago (as indicated by the oldest artifacts excavated on the island) and rapidly became dwarfed.
The discoverers (archaeologist Mike Morwood and colleagues) proposed that a variety of features, both primitive and derived, identify these individuals as belonging to a new species, H. floresiensis, within the taxonomic tribe of Hominini, which includes all species that are more closely related to humans than to chimpanzees. Based on previous date estimates, the discoverers also proposed that H. floresiensis lived contemporaneously with modern humans on Flores.
Two orthopedic researches published in 2007 reported evidence to support species status for H. floresiensis. A study of three tokens of carpal (wrist) bones concluded there were differences from the carpal bones of modern humans and similarities to those of a chimpanzee or an early hominin such as Australopithecus. A study of the bones and joints of the arm, shoulder, and lower limbs also concluded that H. floresiensis was more similar to early humans and other apes than modern humans. In 2009, the publication of a cladistic analysis and a study of comparative body measurements provided further support for the hypothesis that H. floresiensis and Homo sapiens are separate species.

The ideas behind Jurassic Park have become real, kinda sorta. It is now possible
to retrieve and sequence DNA from ancient specimens. Although these sequences are
based on poor quality DNA and thus have many inferential steps (i,e, the resulting
sequence is not likely to be a perfect replica of the living DNA), the insights to
be gained from paleosequentcing are nonetheless great. For example, paleo-sequencing
has shown that Neanderthal DNA is sufficiently different from human DNA as to be
reasonably considered as coming from a different species.

PUBMED QUERY: "ancient DNA" OR "ancient genome" OR paleogenetic OR paleogenetics NOT pmcbook NOT ispreviousversion

"A feathered dinosaur is any species of dinosaur possessing feathers. For over
150 years, since scientific research began on dinosaurs in the early 1800s,
dinosaurs were generally believed to be related to the reptile family; the word
"dinosaur", coined in 1842 by paleontologist Richard Owen, comes from the Greek
for "formidable lizard". This view began to shift during the so-called dinosaur
renaissance in scientific research in the late 1960s, and by the mid-1990s
significant evidence had emerged that dinosaurs are much more closely related
to birds. In fact, birds are now believed to have descended directly from the
theropod group of dinosaurs, and are thus classified as dinosaurs themselves,
meaning that any modern bird can be considered a feathered dinosaur, since all
modern birds possess feathers (with the exception of a few artificially selected
chickens).
Among extinct dinosaurs, feathers or feather-like integument have been discovered
on dozens of genera via both direct and indirect fossil evidence. The vast majority of
feather discoveries have been for coelurosaurian theropods. However, integument has
also been discovered on at least three ornithischians, raising the likelihood that
proto-feathers were also present in earlier dinosaurs." QUOTE FROM:
Wikipedia

PUBMED QUERY: (dinosaur OR dinosaurs) AND (feather OR feathers OR feathered OR plumage OR pigmentation OR pigment OR countershading) NOT pmcbook NOT ispreviousversion

Clustered regularly interspaced short palindromic repeats (CRISPR, pronounced
crisper) are segments of prokaryotic DNA containing short repetitions of base
sequences. Each repetition is followed by short segments of "spacer DNA" from
previous exposures to foreign DNA (e.g a virus or plasmid).
The CRISPR/Cas system is a prokaryotic immune system that confers resistance to
foreign genetic elements such as those present within plasmids and phages, and
provides a form of acquired immunity. CRISPR associated proteins (Cas) use the
CRISPR spacers to recognize and cut these exogenous genetic elements in a manner
analogous to RNA interference in eukaryotic organisms. CRISPRs are found in
approximately 40% of sequenced bacterial genomes and 90% of sequenced archaea.
By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA)
into a cell, the cell's genome can be cut at a desired location, allowing
existing genes to be removed and/or new ones added. The Cas9-gRNA complex
corresponds with the CAS III crRNA complex in the above diagram. CRISPR/Cas genome
editing techniques have many potential applications, including altering the
germline of humans, animals, and food crops. The use of CRISPR Cas9-gRNA complex
for genome editing was the AAAS's choice for
breakthrough of the year in 2015.

PUBMED QUERY: "CRISPR.CAS" OR "crispr/cas" NOT pmcbook NOT ispreviousversion

Fecal Transplantion is a procedure in which fecal matter
is collected from a tested donor, mixed with a saline or other solution, strained,
and placed in a patient, by colonoscopy, endoscopy, sigmoidoscopy, or enema.
The theory behind the procedure is that a normal gut microbial ecosystem is
required for good health and that sometimes a benefucuial ecosystem can be
destroyed, perhaps by antibiotics,
allowing other bacteria, specifically
Clostridium difficile to over-populate the colon, causing debilitating,
sometimes fatal
diarrhea.
C. diff. is on the rise throughout
the world. The CDC reports that approximately 347,000 people in the U.S. alone
were diagnosed with this infection in 2012. Of those, at least 14,000 died.
Fecal transplant has also had promising results with many other digestive or
auto-immune diseases, including Irritable Bowel Syndrome, Crohn's Disease, and
Ulcerative Colitis. It has also been used around the world to treat other conditions,
although more research in other areas is needed.
Fecal transplant was first documented in 4th century China, where the treatment was
known as yellow soup.

PUBMED QUERY: "(fecal OR faecal) (transplant OR transplantation)" OR "fecal microbiota transplant" NOT pmcbook NOT ispreviousversion

"Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the mechanisms of their formation and how they exert their regulatory effect on embedded genes. Further, similar domains have been detected in other organisms, including flies, worms, fungi and bacteria. Although in all these cases these domains appear similar as detected by 3C-based methods, their biology appears to be quite distinct with differences in the protein complexes involved in their formation and differences in their internal organization."
QUOTE FROM:
Dekker Job and Heard Edith (2015), Structural and functional diversity of Topologically Associating Domains, FEBS Letters, 589, doi: 10.1016/j.febslet.2015.08.044

Wikipedia:
A formant, as defined by James Jeans, is a harmonic of a note that is augmented
by a resonance. In speech science and
phonetics, however, a formant is also sometimes used to mean acoustic resonance
of the human vocal tract. Thus, in phonetics, formant can mean either a resonance
or the spectral maximum that the resonance produces. Formants are often measured
as amplitude peaks in the frequency spectrum of the sound, using a spectrogram
(in the figure) or a spectrum analyzer and, in the case of the voice, this gives
an estimate of the vocal tract resonances. In vowels spoken with a high fundamental
frequency, as in a female or child voice, however, the frequency of the resonance
may lie between the widely spaced harmonics and hence no corresponding peak is visible.
Because formants are a product of resonance and resonance is affected by the
shape and material of the resonating structure, and because all animals (humans
included) have unqiue morphologies, formants can add additional generic (sounds big)
and specific (that's Towser barking) information to animal vocalizations.

The notion of "conditioned taste aversions" refers to animals' ability
to preferentially associate taste with illness, despite the passage of
a significant time between ingestion and illness. When first described,
this pattern seemed
so at variance with the tenets of classical learning theory that one
early reviewer claimed "results like that are no more likely
than birdshit in a cuckoo clock." Now, however, the reality of the
phenomenon is well established and has demonstrated relevance in
practical areas ranging from rodent control to chemotherapy.

The year 2014 was the hottest year on record, since the beginning of
record keeping over 100 years ago. The year 2015 broke that record,
and 2016 will break the record of 2015. The Earth seems to be on a
significant warming trend.

Mesothelioma is a rare, but deadly form of cancer that is often
(nearly always) associated with prior exposure to asbestos. The
latency between exposure and disease onset is long, usually 20-50
years, making this a difficult cause-effect system to study.

PUBMED QUERY: asbestos AND mesothelioma NOT pmcbook NOT ispreviousversion

RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served
as a tenured faculty member in the Zoology and Biological Science
departments at Michigan State University. He is currently exploring
the intersection between genomics, microbial ecology, and biodiversity
— an area that promises to transform our understanding of the
biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he
taught introductory biology, genetics, and population genetics. At
JHU, he was an instructor for a special course on biological database
design. At FHCRC, he team-taught a graduate-level course on the
history of genetics. At Bellevue College he taught medical
informatics.

Administrator

Robbins has been involved in science administration at both the
federal and the institutional levels. At NSF he was a program officer
for database activities in the life sciences, at DOE he was a program
officer for information infrastructure in the human genome project. At
the Fred Hutchinson Cancer Research Center, he served as a vice
president for fifteen years.

Technologist

Robbins has been involved with information technology since writing
his first Fortran program as a college student. At NSF he was the first
program officer for database activities in the life sciences. At JHU
he held an appointment in the CS department and served as director of
the informatics core for the Genome Data Base. At the FHCRC he was VP
for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing
venture, founding a small company that addressed the short-run
publishing needs of instructors in very large undergraduate classes.
For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project,
a web site dedicated to the digital publishing of critical works in
science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called
upon to provide keynote or plenary addresses at international
meetings. For example, in July, 2012, he gave a well-received keynote address at the
Global Biodiversity Informatics Congress, sponsored by GBIF and held
in Copenhagen. The slides from that talk can be seen
HERE.

Facilitator

Robbins is a skilled meeting facilitator.
He prefers a participatory approach, with
part of the meeting involving dynamic breakout groups, created by the
participants in real time: (1) individuals propose breakout groups;
(2) everyone signs up for one (or more) groups; (3) the groups
with the most interested parties then meet, with reports from each
group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s,
when he worked for a professional photography laboratory. He now
prefers digital photography and tools for their precision and
reproducibility. He designed his first web site more than 20 years
ago and he personally designed and implemented this web site.
He engages in graphic design as a hobby.

Reprints and preprints of publications, slide presentations,
instructional materials, and data compilations written or
prepared by Robert Robbins. Most papers deal with
computational biology, genome informatics, using information
technology to support biomedical research, and related matters.

ResearchGate is a social networking site for scientists and
researchers to share papers, ask and answer questions, and
find collaborators. According to a study by
Nature
and an
article in
Times Higher Education
, it is the largest academic
social network in terms of active users.